I think that my implementation of the "only one way" doesn't work in the face of multiple libraries with identical column lookup names. What I did was prevent the user from updating the fields, thus ensuring that CC could not sync new values to calibre. Unfortunately, what you are doing is a different thing, having the "same" custom column in multiple libraries with different values. Connecting to one library and then to another is syncing the first to the second with no user modification of the information. I need to look at how to deal with this.
My recommendation is that because you are using multiple libraries with different content, you do not enter read column information until such time as I find a fix for this use case.
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